דברי הקבלה אין בהן מחלוקת לעולם, וכל דבר שתמצא בו מחלוקת בידוע שאינו קבלה ממש רבינו
The obvious question is the machlokes between Rabbonon and Sumchos by chatzi nezek of tzeroros, which is clearly a machlokes on a halacha l'moshe misinai. The maharatz chiyus quotes this question from the Chavos Yair (192), and suggests based on the pirsuh hamishna of the rambam at the end of edyos where the rambam writes that we have a tradition that Eliyahu Hanavi will do good for klal yisroel at the end of time, but there is a machlokes on the specifics. Here too, all agree that tzroros is a halacha l'moshe misinai that it is included in damages that one is responsible for, but they argue how much one is chayev.
The difficulty with the approach of the maharatz chiyus is that R' Ashi asks according to Sumchos whether the halacha l'moshe misinai of tzroros applies to "koach kocho" according to sumchos. This question only makes sense if we assume that kocho is like gufo, and it is obvious without any halacha l'moshe misinai that one should pay full, but "koach kocho" may not be like gufo and we can apply the halacha l'moshe misinai to reduce the payment to chatzi nezek. It is also clear in Rabbeinu Chananel 19a, that the question of "koach kocho" is whether sumchos agreees to the halacha l'moshe misinai and applies it to koach kocho, or does he reject the halacha l'moshe misinai entirely.
The Chasam Sofer (Beitza 5a - pg. 20) offers another approach. We certainly find many cases of machlokes about halacha l'moshe misinai. The Rambam doesn't mean to say that a machlokes cannot develop on a tradition, rather he means to say that when there was a machlokes about a tradition and the rabbonon of the generation agree to one approach and reject the other, essentially deciding that the tradition of the one they accept is correct and the other is not. At that point, no later generation can restore the machlokes and rely on the tradition of the yachid (which can be done by an argument that develops from 13 midos).